A Certain Phantom Sister
by RedOmega
Summary: A Sister clone under the command of the Superintendent himself is sent to the city of Tokyo and attend high school for unknown reasons. However, after meeting a certain frizzy-haired boy, things take a drastic turn that seems to be incomprehensible even for science.
1. Chapter 1: Tokyo

**Welcome to my Persona 5×Toaru Majutsu no Index/Kagaku no Railgun Fanfiction! Just so you guys know, the main character is an OC Sister and isn't part of the main unit of Sister clones.**

 **I've never read the novel so I'm just using my knowledge of the Sisters from the anime and the Railgun manga, though, I did do my research of things that are yet adapted to the manga and anime.**

 **So I hope you all relax and enjoy!**

* * *

"You _will be transferred to Tokyo, do you understand?"_

 _A certain young female who seemed to be around the age of 17 asked the figure standing firmly in front of her. Despite appearing to be a high school student, instead of her designated school uniform, she wears a lab coat of a scientist. Her unkempt black hair and aloof eyes make her seem to be an unapproachable character. However, her described persona of aloofness is not present but rather it is replaced with an expression of concern._

 _"'Why?' Asks Misaka, desiring to know more information."_

 _Unlike the first one, the second girl looked younger than her, having the appearance of that of a middle-schooler. She had chesnut-brown hair and eyes which looked like that of a lifeless person. Unlike the high-schooler, she wears her school uniform, which is comprised of a long-sleeved white blouse worn under a light brown blazer uniform w_ _ith the school emblem on the left side. For the bottom, she wears a checkered blue skirt with black and tan criss-crossing lines that reach halfway down her thighs as well as sporting black socks and brown loafers._

 _"I don't know. In fact, it was the Superintendent that ordered the transfer." The aloof girl answered before taking out a stack of papers from the pocket of her lab coat and looking at one page to another, "Not only will you just transfer to another city but you will also be attending a school, a high school as a second-year, no less."_

 _"'High school? But doesn't my biological age match that of a middle-schooler like Onee-sama?' Asks Misaka again while tilting her head in confusion."_

 _The black-haired girl shrugged in response, " **Like I said** , I don't know myself. Though, the higher-ups probably convinced the staff in your new school to let you in a high school academy despite your considered age."_

 _"'I see.' Says Misaka as she finally stops asking further questions."_

 _"Look, the place you're going to is going to be a completely new environment for you." The high-schooler told her with a soft look on her face, "You need to be careful, especially since you're alone. Though, I don't get why they didn't assign a guardian to watch over you, at least."_

 _She looked away for a short moment, her face shadowed by her hair bangs, muttering something, "If I knew this would happen, I should have inputted stronger emotions in you."_

 _She dove her hand into the pocket of the left side of her lab coat and took out a dark-blue pocket-sized journal and handed it to the middle-schooler, "Here, this contains instructions on how to live like the others around you and some tips. I think social support would be a lot better for you but since you don't have a guardian assigned to you and I'm not allowed to leave my position, this will have to do. **In addition** , I've also added cooking recipes inside so you can develop your cooking skills."_

 _"'I see. Thank you.' Says Misaka as she bows her head in gratitude."_

 _" **Also** , there's one more thing I want to give you."_

 _"'What is it?' Asks Misaka."_

* * *

 **[Update: Misaka 7191 has been eliminated]**

A certain brown-haired girl opened her eyes when the words of a female voice with a robotic tone registered in her mind. She stood up from her bed and neatly fixed the arrangement of her bedding. Opening her closet, she took out her uniform which is a beige turtle-neck sweater and a black blazer with red buttons along with the symbol of her current school located at the chest part of the clothing. Her black skirt is the same size as her previous one but this one has a tartan design pattern with red and white linings. She placed them neatly on her bed and she took out a long towel from her closet before closing it and going to the shower.

After less than 20 minutes in the shower, the girl came out with the towel wrapped around her. She started to put on her underwear before dressing up in her school uniform along with her long black socks. She then opened a drawer of a stand located right beside her bed and pulled a small blue journal before closing the drawer. She began to flip the pages one by one before suddenly starting to skim through most of the pages which she suddenly stopped. She read the pages for a few minutes as she went towards the stove and opened a refrigirator, taking out some ingredients required for her cooking. She placed her journal on the dining table and left it open where it was at the page of a recipe.

She began her process of cooking for the first time without anyone's help, looking at the open journal every few minutes while cooking. The process took about 30 minutes since she cooked food for both breakfast and lunch, which the latter is put inside a bento box. She took a long stare at her breakfast, which is a tamagoyaki (japanese omelet), and the lunch in her bento, which is hamburger steak with broccoli, tomato, celery sticks and corn as well as rice with furikake along with some strawberries in a seperate container. She took a look at the picture of the recipe and then the real version through her cooking, which perfectly match, before saying her first words of today.

"'Excellent.' Complements Misaka to herself for her accomplishment."

She closed the lid on her bento box as she sat down to eat her first meal for today. After finishing her meal, she washed the dishes and then placed her bento box in her bag.

She took her school bag before opening the shoe rack and taking out her brown loafers and putting them on. She closed the door of the shoe rack and turned off the lights as she closed the door of her apartment.

* * *

Once outside, she took a moment to look out at the scenery of the surroundings of the building she's living in. Yongen-Jaya is known as one of the heavily populated residential districts in Tokyo, as such she can see many people going to work as well as students going to different schools. This kind of scene in the morning is no different from that of Academy City, though, if she could tell the difference between them it would be that the people are mostly students rather than adults. She noticed that many of them are going to the same direction, which is the train station.

"'It looks like the trains will be heavily crowded.' Says Misaka as she sighs in frustration."

Though she says that, there was no hint of frustration on her face. All one could see is an emotionless expression along with some lifeless eyes. She went to the elevator, it would take more time if she went to the stairs.

She exited the elevator and began walking through the backstreets of Yongen-Jaya. Looking around, the appearance of the area look similar to that of School District 10 in Academy City, except that the district is a hot bed for delinquents and Level 0s as well as the fact that it was filled with things like disposal areas for experimental animals and laboratories related to nuclear power.

As she continued to walk, she notices a young man wearing the uniform of her school walk out of a café called "Leblanc" and flip the door sign from 'close' to 'open'. She passes him by and he didn't seem to notice her walking pass him since he seems to be focused on something else.

She took a left turn and descended down the stairs which led to the Yongen-Jaya Subway Platform as she heard a robotic, female voice but it is not the same one from earlier.

 **[Yongen-Jaya. This is Yongen-Jaya.]**

The train seemed to have just arrived as many workers came out of the train. The girl waited for a bit so that she wouldn't bump to most of the people coming out and soon, she walked in. As she stepped a foot inside the train she felt someone bump her from behind her shoulder. She turned around and saw that it was the same young man from the café, his black frizzy hair and glasses being his most prominent features which the girl took note of.

"Ah, I'm sorry." The boy said as he bowed apology.

Tilting her head slightly, the girl responded, "'It's okay.' Says Misaka as she accepts your apology."

The boy adjusted his glasses as he let out a somewhat quizzical expression on his face. He was puzzled by her strange way of speaking in third-person. Is it a verbal tic, perhaps? Although, his thoughts were interrupted when more people began boarding the train. The two of them didn't managed to get a seat and soon, the people inside got packed like a can of sardines.

The train then left the station and the two stayed silent for a few minutes while managing to breath normally despite the inside being too crowded and tight before the brown-haired girl suddenly spoke up.

"'Are you a student of Shujin Academy?' Asks Misaka for confirmation after seeing your school uniform."

Again, the boy became somewhat puzzled due to her way of speech but kept his composure, "Yes, I am."

"'I see.' Says Misaka as she accepts your answer."

An awkward silence then followed, at least for the young man, the girl kept an emotionless expression the whole time which makes it very difficult for anyone to guess what's on her mind.

"Er, my name is Kurusu Akira, it's a pleasure to meet you." Strange, he usually wasn't the kind of person that would start a conversation. But there seems to be something about the girl that intrigued him.

"'I am Misaka...'"

There was a sudden pause for a moment.

"'...Imouto. Misaka Imouto. A pleasure to meet you as well, Kurusu-san.' Says Misaka as she introduces herself to her new schoolmate."

New schoolmate? Did she know that he's a transfer student or was it the other way around? Then again, now that he looked at her closely, she looked like a middle-schooler but since she's attending the same school as him, maybe she's a first-year? Also, her name is rather strange as well, would someone actually name their child from a noun? He mentally shook these thoughts out of his head, thinking that he'll find out soon once they get to school.

His vision took a good look at all around the inside of the train.

 _"There are so many people crammed into this tiny car. It turns out the rumors about the Tokyo subway are true..."_

His gaze turned to the LCD screen of the train, which is showing the news about yesterday's accident as well as the lingering effects of it. He turned to look at Misaka, who is also staring at the screen with an unchanging expression.

The train then came to a stop after a few minutes.

 **[Shibuya. This is Shibuya.]**

The two Shujin students made their way to the opened doors. Misaka nearly fell to the ground due to the constant bumping of the people making their way out of the train, Akira barely managed to grab her arm and pull her before she fell.

"Are you okay?"

Misaka nodded in assurance, "'Yes. Thank you.' Answers Misaka in gratitude."

"'We have to change to the Ginza Line, correct?' Asks Misaka because of the fact that this is her first time here."

"Yeah." Akira nodded, "Although, I'm not sure where since this is my first time here too."

"'I see. Then let's make our way upstairs and ask for directions.' Suggests Misaka."

Akira nodded in agreement as they walked upstairs towards the Underground Walkway. Once they reached the top, they noticed a crowd of people near the row of fare adjustment machines. They must be waiting for a train but is late due to the accident yesterday. As they walked closer, they could hear a man arguing with an exhausted station attendant.

"Why is it late again? The accident was yesterday."

"Our apologies." The attendant bowed in apology, "However, it was a major accident and-"

The man cut him off, "This isn't the first time this happened. Why weren't you better prepared for this one? Sheesh..."

Seeing that since there are many people here, Akira used this opportunity to finally ask for directions, "Excuse me..."

A man who seemed busy with his phone turned to Akira with a raised eyebrow, "Hm? What is it?"

"Do you know where the Ginza Line is?"

"Oh, just head over there." The man replied pointing a finger to the area by the right, "It's in Exit 8, you can see the yellow sign if you look to your right from there. Once you arrive at the Station Square, it's in the Teikyu Building."

"I see. Thank you very much." Akira politely bowed in gratitude along with Misaka, even though she didn't say anything.

The two walked towards the pointed direction and they swiped their IC cards through the ticket gate and stopped where they took a look around looking for a certain sign. Misaka then stops and point at a yellow rectangular sign with a large 8 on it.

"'Over there.' Directs Misaka, pointing to where Exit 8 is."

Akira turned to where Misaka was pointing and nodded. Immediately, they speedwalked towards the next area and walked up through the escalator. Once arriving at the top, they turned their direction to the large staircase on the right side since the JL ticket gates are on the left and the passage on the front has a sign which says that they are cleaning the area right now. They walked up the large staircase towards the Station Square.

Now at a new area, the two found the Teikyu Building that was mentioned earlier right in front of them and made their way to it, only to stop for a moment once they saw a reporter and a cameraman filming rght in front of the Shibuya Station.

"We're coming to you live from Shibuya Station." The reporter started, "The cause of yesterday's subway derailment has affected all transportation lines. The string of accidents has put commuters on high alert..."

While it was interesting to listen to it, they have no time to waste so they proceeded to their next destination in the building in front of them. They hurriedly proceeded upstairs and swiped their IC cards to the next ticket gate that leads to the yellow train past the next staircase.

Once they enter the train, the two of them managed to find a wide-open seat near the doors and they immediately sat before they get tightly surrounded like in the previous train. They waited for a while until they get to their final stop.

*Beep* *Beep*

Hearing the beeping sounds, Akira took out his phone from his pocket and saw that it was on low battery in 10%.

 _"Ah, crap. I forgot to charge this earlier..."_ Akira sighed.

Misaka turned to him then to his phone where she saw the notification of low battery.

"'Give it to me for a moment.' Demands Misaka after seeing the state of your phone."

Akira turned to her with a raised eyebrow in confusion, "Huh? Why?"

"'I will not have the time to explain it fully once we reach the next stop.' Says Misaka while still demanding to hand over your phone."

"Your way of wording sounds so wrong right now." The frizzy-haired boy commented, though, he complied to the strange girl's demand.

Silence followed for a few minutes with Misaka seemingly staring at the phone while holding it close. However, for a moment, Akira swore that he just saw a small spark of electricity coming from the phone and the next thing he knew, his phone's battery is now at 100%.

"Huh?" Wait, how did that happened? Did he just see his phone's battery go from 10% to 100% in a few minutes? What did she do? He was sure that Misaka was just staring at the phone the whole time she was holding it. Did she use some sort of wireless power bank or something?

Misaka handed back the phone with that still indifferent expression on her face.

"Uh, thanks." Akira thanked her, still confused, he was about to ask how she did it until a certain app from his phone caught his attention.

It was the strange app with the creepy eye.

 _"What the hell? I've deleted this app twice now..."_

He proceeded to drag the disturbing app towards the trash bin without hesitation, _"I really need to reboot this phone later."_

A few seconds later, they felt the train stopping and soon heard a male, robotic voice as the train doors open.

 **[Aoyama-Itchome. This is Aoyama-Itchome]**

The two stood and walked alongside the crowd of people going out the train. As soon as they stepped outside the yellow train, Akira let out a sigh of relief.

"It took some time, but we finally made it..."

"'I agree. It is quite tiring to do this everyday.' Says Misaka as she agrees to your comment."

Akira seemed to have gotten used to her way of speaking rather quickly despite having only just met earlier today. Normally, most people who would get weirded out by someone's unique quirk would rather avoid being close to such strange people. However, at this point, Akira concluded for now that it's probably just her verbal tic.

The two looked around and immediately saw many students in the subway platform wearing the same uniform as theirs. They heard some of the chatting students' conversation that it is starting to rain. Of all days it had to rain, it had to be at the start of their first day. The two transfer students swiped their cards through the ticket gate leading to Shujin Academy as he and Misaka immediately hurried upstairs to the path towards Shujjn Academy. Unfortunately, they were met with a heavy rain and they were forced to take shelter under a roof of a nearby dressing store as they watched their fellow schoolmates run through the rain with umbrellas in hand.

Akira decided to check his phone to check the time to make sure they weren't late just yet, however, the app that he just deleted earlier came back again, this time it took over half the screen which caused him to sigh in frustration, _"And here I thought t_ _hird time's the charm..."_

As he was about to drag it straight to the trash bin again, a sudden arrival of a female Shujin student distracted him as she took shelter under the roof as well. Her school uniform seems to be modified as it appears to be vastly different compared to their uniform. She wears the standard black blazer over a white varsity-like fullzip hooded sweatshirt, worn long to cover most of her short plaid skirt. Her sweatshirt has a red stripe between two blue stripes at the bottom, an S symbol near the front bottom on one side and a green four-leaf-clover symbol on the back of the hood. She wears red tights and brown boots with yellow laces. She pulls down her hoodie, revealing her long blonde hair, which is styled in bushy pigtails, and blue eyes which immediately gave her the atmosphere of a foreigner.

Akira stared at her in surprise, somewhat intrigued to have learned that a person like her is his schoolmate. As for Misaka, she only looked at the blonde foreigner momentarily before focusing her gaze at the road with her still unchanging expression of indifference. The blonde noticed his gaze and smiled at him before focusing on the road.

A few seconds later, a silver car suddenly stops in front of them and the front window slides down, showing a rather large-looking man with black unkempt hair and thick eyebrows. His jawline is broad and square and wears a blue jumpsuit. He leaned towards the window and smiled, "Good morning. Want me to give you a ride to school? You're gonna be late."

The blonde smiled back, although it appeared to be forced, "Um, sure. Thank you."

The man turned to Misaka with his unchanging charming smile, "What about you, little lady? You're gonna get wet if you have to walk through this rain."

Misaka politely bowed, "'There's no need. Thank you for your offer.' Declines Misaka."

The man and the blonde girl, who turned to Misaka briefly, both have raised eyebrows by her rather strange response as if she were a robot. The man shrugged and turned to Akira next but kept a friendly expression, "Do you need a lift, too?"

Akira seemed to have just noticed that he was being addressed to and he, like Misaka, politely declined, "Hm? Ah, no thanks."

The man adjusted his seat belt as the blonde sat in her seat and closed the door. Just before the window closed completely, the two transfer students noticed the strained expression on her face as if she's being forced before the car drove away.

"Dammit!"

Another blonde teenager appeared in the scene, although unlike the girl, the spiky hair of the boy appeared to be dyed and had dark brown eyes. However, like the blonde girl, he wears his winter school uniform a bit modified. It consists of the standard black blazer, unbuttoned to reveal a yellow t-shirt with a comic style star symbol and the word 'ZOMG!' He has plaid trousers rolled up to reveal his ankles. His pants have black suspenders that hang down instead of being worn on his shoulders. He has a white belt. His white sneakers have a rising sun flag motif.

The vulgar boy scowled as he watched the car drove away and muttered angrily, "Screw that pervy teacher..."

"...Pervy teacher?" Akira absentmindedly repeated. Unbeknownst to him, the disturbing app on his phone was still active and it recorded his sentence.

The vulgar boy noticed and turned to the two of them and glared as he marched over to them, "What do you want? You plannin' on rattin' me out to Kamoshida?"

"Kamoshida?" Akira tilted his head in confusion, not knowing who the blonde was referring to.

"Huh?" This time, it was the vulgar boy's turn to be confused by the frizzy-haired boy's reaction, "In that car just now. It was Kamoshida." He then frowned and began to criticize the said person, "He does whatever the hell he wants. Who does he think he is-the king of a castle? Don't you agree?"

Still confused, Akira wasn't sure what kind of response he should give. However, before he could give an answer, Misaka barged in the conversation.

"'We do not know who Kamoshida is.' Answers Misaka."

The blonde raised an eyebrow, "What's with the weird way of talking? And wait... you don't know him? Are you for real? I mean, you guys're from Shujin, right?"

"'We are transfer students.' Explains Misaka."

The blonde had a flash of realization, "Oh! Then no wonder you two don't know him. Let me guess, you a second-year?"

Akira nodded.

The blonde let out a smile, "Huh. Same grade as me." He then turned to Misaka, "Let me guess again... you look like a middle-schooler, so you're a first-year, right?"

Misaka shook her head, "'Incorrect. I'm a second-year as well.' Answers Misaka."

The blonde's eyes widened in surprise, "Seriously?! Did you skip a grade or something?"

"'Something like that.' Answers Misaka vaguely."

The blonde (Jesus, how many times have I wrote that word?) then stared at the cloud-covered sky and notices that the rain is about to let up, "This rain ain't too bad. We better hurry up, or we'll be late."

However, just as the three of them are about to proceed, pain welled up inside their heads.

"Ngh..." Misaka placed her hand to her head and the pain in her head immediately left her, _"Is there some abnormality in the network?"_

"Uuugh, my head hurts..." The vulgar boy groaned as he began to walk away, "Dammit... I wanna go home..."

"..." Akira, ignoring the headache he just had, followed him. However, he noticed that Misaka isn't moving from her spot, "What's wrong?"

"'...It is nothing.' Assures Misaka." She then held her school bag above her head so at least her hair won't get wet.

The two transfer students then followed the blonde boy, who went to a different path than the other students. They went to an alleyway where they followed the delinquent. However, Akira suddenly halted, causing Misaka to stop behind him.

"'What's wrong?' Asks Misaka." She said while tilting her head.

"Ah, it's... nothing. I thought I just heard something weird." He explained.

"'It must have been your imagination.' Says-" Before she could finish her sentence, a loud cry whose voice they recognized.

"Wha...!?"

They suddenly heard the delinquent's exclamation and they hurried to his spot. However, the sight the met them was unbelievable.

...What stood before them was a castle.

It looked like something that came from a fantasy game but they could tell from the lifelike structure that it is real. However, what truly stood out in the image of the castle was the sign that confirms the location before them as "Shujin Academy".

"We didn't come... the wrong way, though." The blonde uneasily said as both he and Akira looked back towards the path they just took. He turned his gaze towards the front stone sign, "Yeah, this should be right."

"'Is there some sort of event today?' Asks Misaka." She looked back at the bizarre castle.

"Not that I've heard of..." The blonde replied, "What's goin' on...?" Sighing, he turned to the two transfer students, "I guess we'll just have to go and ask."

Akira and Misaka nodded in agreement as the three of them walked towards the drawbridge, with Misaka cautious of what might come.

* * *

 **Before you ask, no, this is NOT Misaka 10032. Like I said, this is an OC Sister. In the first place, "Misaka Imouto" is just what Touma calls her whenever they meet, which means "Misaka's little sister", so it's more of a title rather than a nickname, at least that's what I think.**

 **I tried looking into more japanese names but I didn't want to give my OC a random name with a meaning that didn't match what she is so I decided to use the word "Imouto", since she IS Misaka's little sister.**

 **I'm not sure whether you like her name or not but that is my final decision.**

 **Also, I might add some things from the Toaru Kagaku no Accelerator manga, possibly the characters.**

 **Anyways, thank you for reading the first chapter! :D**


	2. Author's Note

**Hi, RedOmega here! I transferred my story to Wattpad because I want to do illustrations of the story, kinda like a light novel. Sorry for the sudden announcement and I won't be able to update frequently because of school.**

 **I've already published the character profile of my OC so you'll know who she is.**


	3. Author's Note 2

**Ah, fuck it. After reading your reviews I realized that Wattpad has a very shitty search engine and I couldn't fix the problem because I'm no internet expert. I take back what I said about transferring this story to Wattpad so I guess I can't upload any of my illustrations T_T. But I plan on turning my first illustration of my OC as my cover. I'll update the characer profile of my OC soon (maybe the day after tomorrow or something) you'll know who she is and also because I'm too lazy to make a scene that reveals who she is.**

 **Note: Don't expect the update to be frequent because I'm working on another story about Persona 5. I know it's difficult to write multiple stories at the same time but whenever I get a new idea of a story, before I knew it, I'm already making a draft!**


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